AFNI HISTORY
all levels
The levels of importance go from 1 to 5, with meanings:
1 - users would not care
2 - of little importance, though some users might care
3 - fairly important
4 - a big change or new program
5 - IMPORTANT: we expect users to know
generated via the command : afni_history -html -reverse -type NEW_OPT
---- log of AFNI updates (most recent first) ----
23 Nov 2009, RW Cox, 3dmaskSVD, level 1 (MICRO), type 2 (NEW_OPT)
Add -bpass option
23 Nov 2009, RW Cox, 3dTcorrMap, level 1 (MICRO), type 2 (NEW_OPT)
Add various options in the last few days
* -seed = a different dataset for the seed time series
* -bpass = instead of -polort
* -Gblur = blurring
* -Mseed = extra smoothing around the seed
* -Hist = output the histogram of the correlations
20 Nov 2009, DR Glen, 3dAutomask, level 2 (MINOR), type 2 (NEW_OPT)
apply_prefix option to save automasked input
avoids 3dcalc step that is usually used to apply an automask.
17 Nov 2009, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT)
SUMA now handles labeled datatets in a special manner
An example of a labeled dataset would be FreeSurfer's annotation files.
If an annotation file is present in the spec file (@SUMA_Make_Spec_FS),
SUMA will display it as part of the background.
You can chose to display the labeled dataset in color, contours, or both.
Data from labeled datasets is now shown under the 'Lbl' field in the
surface controller's Xhair block.
17 Nov 2009, ZS Saad, ROI2dataset, level 2 (MINOR), type 2 (NEW_OPT)
Option -label_dset creates a labeled dataset from ROIs.
Labeled datasets are now rendered in a special manner in SUMA
17 Nov 2009, ZS Saad, FSread_annot, level 2 (MINOR), type 2 (NEW_OPT)
Option -dset creates a labeled dataset from annotation file.
Labeled datasets are now rendered in a special manner in SUMA
17 Nov 2009, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
Script now automatically sets up the spec file with labeled datasets
Labeled datasets are created from annotation files,
and are now rendered in a special manner in SUMA
09 Nov 2009, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT)
Added options to check for, and correct 'bowties' in pathches.
Bowties in patches result in non 2-manifold stiched surfaces whose
volume cannot be caluclated. The *bowtie option deal with such cases.
09 Nov 2009, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT)
Added options to shrink patch contours at nodes not in selected nodes.
See options -adjust_contour for details.
09 Nov 2009, ZS Saad, SurfMeasures, level 2 (MINOR), type 2 (NEW_OPT)
Added option for improved node volume estimation.
The new measure, called node_volg, uses Gauss' Theorem to estimate
the volume associated with a node in two isotopic surfaces. This option
is more robust to surface curvature variations.
04 Nov 2009, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT)
3dAllineate option for motion correction
volreg_method allows 3dAllineate, which is useful for DTI data.
Bug fix for post-transformation matrix and dataset view
27 Oct 2009, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
added support for optional LabelTable RGBA attributes
23 Oct 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -censor_fill and -censor_fill_par
These options are to zero-pad TRs that were censored by 3dDeconvolve.
19 Oct 2009, RW Cox, 3dBlurInMask, level 1 (MICRO), type 2 (NEW_OPT)
add -preserve option, to keep Rick Reynolds from defecting to SPM
19 Oct 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added options for using 3dBlurInMask, instead of 3dmerge
- added -blur_in_mask, -blur_in_automask and -blur_opts_BIM
- added -sep_char and -subj_curly
19 Oct 2009, DR Glen, align_epi_anat.py, level 3 (MAJOR), type 2 (NEW_OPT)
New master options, dset1/2 terminology
New master_nnn_dxyz options to specify output resolution
dset1 and dset2 for non-EPI/anat alignment with lpa cost function
and turns off preprocessing steps
giant_move option turns off resampling and changes master options
Expanded help - including fuller description of edge method
Removed volume registration (motion correction) for anat2epi option
by default.
AFNI dataset views (+orig/+acpc/+tlrc) are maintained in output
depending on BASE, SOURCE or external dataset names for all output
16 Oct 2009, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT)
added -demean, to demean motion parameters, for example
The polort 0 values should be more accurate baseline constants.
Useful for creating a proper polort baseline w/3dSynthesize.
13 Oct 2009, ZS Saad, quickspec, level 1 (MICRO), type 2 (NEW_OPT)
-tsnad to allow for setting anatomical flag and local domain parent
13 Oct 2009, ZS Saad, ConvertSurface, level 1 (MICRO), type 2 (NEW_OPT)
-xmat_1D allows for single row transform definition
07 Oct 2009, ZS Saad, 1dplot, level 1 (MICRO), type 2 (NEW_OPT)
1dplot's window frame now shows a title. See 1dplot -wintitle for details.
07 Oct 2009, RW Cox, 3dBlurInMask, level 2 (MINOR), type 2 (NEW_OPT)
Add -Mmask option to allow multiple mask values
For independent blurring (e.g., blur WM and GM separately).
06 Oct 2009, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT)
added -set_run_lengths option, for varying run lengths
Added for motion censoring and run padding.
29 Sep 2009, DR Glen, RetroTS, level 2 (MINOR), type 2 (NEW_OPT)
Flexible slice timing options
SliceOrder option allows for standard slice timing order
alt+z, alt-z, seq+z, seq-z, Custom and 1D text file input
29 Sep 2009, DR Glen, McRetroTS, level 2 (MINOR), type 2 (NEW_OPT)
Opt options available to compiled version
All options available through the Opt structure are now available
even with the compiled version of McRetroTS, making the compiled version
functionally equivalent to the RetroTS.m version
24 Sep 2009, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Improved the 'star' blurring interface.
18 Sep 2009, ZS Saad, SurfClust, level 2 (MINOR), type 2 (NEW_OPT)
Added option -n minnodes
18 Sep 2009, ZS Saad, FSread_annot, level 2 (MINOR), type 2 (NEW_OPT)
Allow specifying external FreeSurfer color table.
16 Sep 2009, RC Reynolds, timing_tool.py, level 1 (MICRO), type 2 (NEW_OPT)
added -scale_data for J Meltzer
16 Sep 2009, RC Reynolds, plug_vol2surf, level 1 (MICRO), type 2 (NEW_OPT)
can init debug level via AFNI_DEBUG_PLUG_VOL2SURF
14 Sep 2009, ZS Saad, SurfClust, level 2 (MINOR), type 2 (NEW_OPT)
Allow specifying rmm in number of edges connecting nodes.
09 Sep 2009, ZS Saad, @fast_roi, level 2 (MINOR), type 2 (NEW_OPT)
Allow @fast_roi to accept existing TLRC transformed anatomy
09 Sep 2009, RW Cox, 3dmaskdump, level 2 (MINOR), type 2 (NEW_OPT)
Add 'ball' options for mask generation
09 Sep 2009, RW Cox, 3dmaskave, level 1 (MICRO), type 2 (NEW_OPT)
Add box and ball options to this program, per Kyle Simmons
04 Sep 2009, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
registration can now be consistent across runs
Reg Base can be 'Current': to set the base volume from the current run
(call this the old way), 'Current & Keep': use current run, but then
store that base and apply it to future runs, 'External Dataset': fix the
base from some chosen dataset.
Using 'Current & Keep' makes sense for realtime registration.
04 Sep 2009, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 2 (NEW_OPT)
if wget fails, try curl; added -curl and -testing options
27 Aug 2009, RC Reynolds, afni_proc.py, level 1 (MICRO), type 2 (NEW_OPT)
added -regress_local_times, -regress_global_times
Since the -local_times and -global_times options in 3dDeconvolve must be
processed before the stimuli they refer to, it does nothing to pass them
via -regress_opts_3dD. Hence, the options are needed.
24 Aug 2009, RW Cox, 3dAFNItoNIML, level 1 (MICRO), type 2 (NEW_OPT)
Add -ascii option == way to dump dataset in plain text
21 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_censor_motion and -regress_censor_prev
Motivated by L Thomas and B Bones.
21 Aug 2009, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 2 (NEW_OPT)
added -show_censor_count
20 Aug 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added motion censoring options
Added -censor_motion, -censor_prev_TR, -collapse_cols, -extreme_mask,
-set_tr, -write_censor and -write_CENSORTR.
Also modified afni_util.py, lib_afni1D.py and option_list.py.
14 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -align_epi_ext_dset, to align anat to external EPI
This may be important for multi-channel coil EPI data with low internal
structural contrast. Users might align to the first (pre-steady-state)
TR, even though that volume is not used in the analysis.
13 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -volreg_tlrc_adwarp, to apply a manual Talairach transformation
04 Aug 2009, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 2 (NEW_OPT)
added basic demo interface and itemized exception traps
27 Jul 2009, RC Reynolds, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
added -slibase_sm, for slice-major ordering of regressors
RetroTS and afni_proc.py were incorrectly using this ordering.
** Analysis done prior to this probably needs to be re-done.
27 Jul 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_labels and -show_label_ordering
27 Jul 2009, RC Reynolds, plug_realtime, level 1 (MICRO), type 2 (NEW_OPT)
added Y/N AFNI_REALTIME_reset_output_index, to start each dset at 001
Also, changed prefix seperator to double underscore '__'.
23 Jul 2009, RW Cox, 3dTfitter, level 1 (MICRO), type 2 (NEW_OPT)
Added -errsum option, to save error sums per voxel.
And a -help example showing how the error sum of squares can be used to
compute partial correlation coefficients of a fit.
23 Jul 2009, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -partition option
23 Jul 2009, DR Glen, MEMRI models, level 2 (MINOR), type 2 (NEW_OPT)
Single and Dual exponential models
New models for 3dNLfim that use single and dual exponential models
that are appropriate for MEMRI (Manganese Enhanced MRI
16 Jul 2009, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
Added option to force autoscale on the graphing window
The option is accessible by pressing 'A' in the graph window
or under 'Graph->Opt->Scale->AUTO'.
14 Jul 2009, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added -max_rest, to limit the maximum duration of rest periods
23 Jun 2009, RW Cox, 3dTcorrMap, level 1 (MICRO), type 2 (NEW_OPT)
Add -Pmean option, based on poster I saw at HBM.
17 Jun 2009, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
version 2.0 : call e2a alignment and warp to standard space ready
- mask warped EPI by its extents (at volreg step)
- added -volreg_no_extent_mask, to block this masking
- added 'extents' to list of mask in -mask_apply
- change block dividers to more visual '===' with block names
17 Jun 2009, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added -make_3dd_contrasts and used general accuracy in block durations
16 Jun 2009, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT)
Add '-ytran' option
Apply an expression to the time series, to transform it prior to
plotting. To elide the use of 1deval.
11 Jun 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added masking abilities
- in mask block, try to create anat and group masks
- added -mask_apply option, for choosing mask to apply to regression
- added -align_opts_aea, for extra opts to align_epi_anat.py
29 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -execute and now fail if block options have no corresponding blocks
27 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
updates for alignment/warp/varying run lengths
- added -volreg_warp_dxyz option
- if align a2e, add -no_ss to @auto_tlrc
- for varying run lengths, fixed application of '-volreg_align_to last'
and the -regress_est_blur_* options
(blur estimation loops were modified for this)
- warping to new grid truncates to 2 significant bits (if < 2 mm)
21 May 2009, ZS Saad, imcat, level 1 (MICRO), type 2 (NEW_OPT)
Now output a grayscale 1D version of an image
That is done by adding a .1D to the -prefix parameter.
21 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added 'align' processing block and -volreg_align_e2a option
19 May 2009, ZS Saad, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT)
Added -zerofill and -roisel options
Added options to force output for empty ROIs.
19 May 2009, ZS Saad, 1ddot, level 2 (MINOR), type 2 (NEW_OPT)
Added -okzero to keep program from exiting with all zero input
Added options to force output for empty ROIs.
19 May 2009, ZS Saad, DriveSuma, level 1 (MICRO), type 2 (NEW_OPT)
Modified time out for DriveSuma to 5 minutes
Time out can be controlled by environment variable SUMA_DriveSumaMaxWait
15 May 2009, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
added -volreg_tlrc_warp option: can warp to standard space at volreg step
15 May 2009, RC Reynolds, afni_util, level 1 (MICRO), type 2 (NEW_OPT)
added get_truncated_grid_dim
08 May 2009, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
The script now automatically turns FS annot files to SUMA ROI files
06 May 2009, RW Cox, afni, level 3 (MAJOR), type 2 (NEW_OPT)
First edition of InstaCorr!
Rough around the edges, but gnarly-ific to the level of the first
inaccessible cardinal!
30 Apr 2009, RC Reynolds, vol2surf, level 2 (MINOR), type 2 (NEW_OPT)
return a node v2s time series when afni changes xhair position
29 Apr 2009, ZS Saad, ROI2dataset, level 2 (MINOR), type 2 (NEW_OPT)
-nodelist* options to output node sequence forming ROI
29 Apr 2009, ZS Saad, ConvertDset, level 2 (MINOR), type 2 (NEW_OPT)
-node_select_1D now respects node ordering
29 Apr 2009, ZS Saad, 3dTcorrMap, level 2 (MINOR), type 2 (NEW_OPT)
-VarThresh* options for obtaining counts at different thresholds
28 Apr 2009, RW Cox, 3dDeconvolve, level 2 (MINOR), type 2 (NEW_OPT)
Add duration argument to SPMGx basis functions for deconvolution.
For Tracy Doty, apparently.
15 Apr 2009, RW Cox, 1dplot, level 1 (MICRO), type 2 (NEW_OPT)
Add -thick option
Plus: modify plot_ts.c to thicken the lines used for plotting the labels
(so the fancy characters are filled in a little).
14 Apr 2009, RC Reynolds, NIfTI, level 2 (MINOR), type 2 (NEW_OPT)
added sample nifticlib program: clib_01_read_write.c
11 Apr 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -volreg_regress_per_run
This is to apply the motion parameters of each run as separate regressors.
11 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -derivative and -set_nruns, fixed -show_cormat_warnings typo
11 Apr 2009, RC Reynolds, option_list.py, level 1 (MICRO), type 2 (NEW_OPT)
enhanced special option processing
- added check_special_opts(), to be called before any processing
- renamed -verbose_opts to -optlist_verbose
- added -optlist_no_show_count
11 Apr 2009, RC Reynolds, afni-general, level 1 (MICRO), type 2 (NEW_OPT)
added calls to opts.check_special_opts() in 7 more python programs:
gen_epi_review.py, make_random_timing.py, make_stim_times.py
neuro_deconvolve.py, python_module_test.py, timing_tool.py, ui_xmat.py
10 Apr 2009, RC Reynolds, to3d, level 2 (MINOR), type 2 (NEW_OPT)
added -use_last_elem option for setting DICOM elements
Can also use AFNI_DICOM_USE_LAST_ELEMENT environment variable.
10 Apr 2009, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -use_last_elem option for setting DICOM elements
09 Apr 2009, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
'official' release with RETROICOR processing block: ricor
o added 'across-runs' ricor_regress_method
o added ricor information and usage to help (see 'RETROICOR NOTE')
o maintain unscaled shorts if they are input
o added -ricor_datum
09 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_cormat_warnings and -cormat_cutoff
08 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_rows_cols option
06 Apr 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added support for '.', ',', and space keys, and 'shw_0'
06 Apr 2009, RW Cox, 3dmaskSVD, level 1 (MICRO), type 2 (NEW_OPT)
Modify to allow output of more than 1 singular vector.
Also, make the help more helpful.
06 Apr 2009, RW Cox, 3dLocalSVD, level 1 (MICRO), type 2 (NEW_OPT)
Add -vproj option
To project central voxel onto low-dimensional local SVD space.
02 Apr 2009, RW Cox, 3dTcorrMap, level 2 (MINOR), type 2 (NEW_OPT)
Add -Thresh option
To save a count of how many other voxels are above threshold correlated
with each seed voxel.
01 Apr 2009, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Arrow keys based navigation along surface.
See 'Alt+U-D' section in SUMA's interactive usage help.
31 Mar 2009, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added 'on the fly' dot product computation
This feature is only available with SUMA's -dev
option. It is still in testing mode and its
interface may change. If intrigued, see 'D' key's
help in SUMA's interactive usage help.
31 Mar 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added support for '[' and ']' keys and -view_surf
31 Mar 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -pad_to_many_runs, -reverse
31 Mar 2009, RC Reynolds, option_list.py, level 1 (MICRO), type 2 (NEW_OPT)
added global -verbose_opts option
31 Mar 2009, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT)
added get_typed_dset_attr_list, enhanced decode_1D_ints
26 Mar 2009, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
Support for reading/writing MNI .obj surfaces
25 Mar 2009, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Add -nobout option, to suppress baseline betas from -Rbeta/-Obeta.
Per the request of Michael S Beauchamp, University of Texas.
19 Mar 2009, RC Reynolds, eg_main_chrono.py, level 2 (MINOR), type 2 (NEW_OPT)
added -verbose_opts option, for being verbose during option processing
19 Mar 2009, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
a few additions and changes
- allow container chars (e.g. []) in decode_1D_ints()
- added is_valid_int_list()
- changed str vars to istr (as str is a keyword)
18 Mar 2009, DR Glen, 3dZcat, 3daxialize, level 2 (MINOR), type 2 (NEW_OPT)
NIFTI support
Fixed support for NIFTI output in 3dZcat and 3daxialize
Added -frugal option to 3daxialize to keep old behavior
for AFNI format datasets. Existing -frugal option in
3dZcat imposes 'oldish' behavior too.
12 Mar 2009, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
SUMA talks to matlab.
12 Mar 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_reml_exec and -regress_3dD_stop
One can execute 3dREMLfit and/or 3dDeconvolve. Error blur is from each.
11 Mar 2009, RW Cox, 3dANOVA, level 2 (MINOR), type 2 (NEW_OPT)
Add -mask option to 3dANOVA, 3dANOVA2, 3dANOVA3
10 Mar 2009, DR Glen, 3dLocalstat, level 2 (MINOR), type 2 (NEW_OPT)
Sum option
Sum option (for functional weighting of interiorosity measure)
09 Mar 2009, RW Cox, 3dDeconvolve, level 1 (MICRO), type 2 (NEW_OPT)
Add SPMG1 to -stim_times repertoire, and update help.
09 Mar 2009, RC Reynolds, suma, level 1 (MICRO), type 2 (NEW_OPT)
added -motif_ver option
06 Mar 2009, RW Cox, 3dDeconvolve, level 2 (MINOR), type 2 (NEW_OPT)
Add 'WAV' function (from waver) to -stim_times repertoire.
05 Mar 2009, RC Reynolds, @build.Xlib, level 1 (MICRO), type 2 (NEW_OPT)
change -noinstall option to -localinstall
04 Mar 2009, RC Reynolds, afni, level 1 (MICRO), type 2 (NEW_OPT)
added -motif_ver option
04 Mar 2009, RC Reynolds, @build.Xlib, level 1 (MICRO), type 2 (NEW_OPT)
added -noinstall option
10 Feb 2009, ZS Saad, DriveSuma, level 1 (MICRO), type 2 (NEW_OPT)
Added -anim_dup to slow down movies
02 Feb 2009, ZS Saad, SurfDist, level 2 (MINOR), type 2 (NEW_OPT)
SurfDist now outputs distances from one node to a set of other nodes
02 Feb 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added load_col option to DriveSuma
05 Jan 2009, ZS Saad, MapIcosahedron, level 2 (MINOR), type 2 (NEW_OPT)
Program no longer confined to FreeSurfer surfaces
The program now allows the user to specify any morph sphere,
not just sphere.reg or sphere. This required rewriting much of
of the program's main section but the algorithm for the mapping
remains unchanged.
05 Jan 2009, ZS Saad, CreateIcosahedron, level 1 (MICRO), type 2 (NEW_OPT)
Program uses new Spec writing function and writes different surface formats
10 Dec 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added new options for extra stimuli, RONI and an external volreg base
- allow NIfTI datasets as input (but process as AFNI)
- added -regress_extra_stim_files and -regress_extra_stim_labels
- added -regress_RONI and -volreg_base_dset (for Jill Weisberg)
09 Dec 2008, ZS Saad, @Align_Centers, level 2 (MINOR), type 2 (NEW_OPT)
Added -cm option to allow centering based on the center of mass
04 Dec 2008, RW Cox, 3dDeconvolve, level 2 (MINOR), type 2 (NEW_OPT)
Extend -stim_times_AM2 option to allow multiple amplitudes
24 Nov 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added options -infile_list and -show_sorted_list
The -show_sorted_list option will print a list of files by run/index.
21 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added Options menu, Show Cosmat and GUI help
This is the initial release version, 1.0.
21 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -test_libs option
21 Nov 2008, RC Reynolds, python_module_test.py, level 2 (MINOR), type 2 (NEW_OPT)
removed 'R' from basic test list, and applied verb 2 to base usage
20 Nov 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
incorportated real-time volume writing from V. Roopchansingh of MCW
18 Nov 2008, RW Cox, 3dANOVA programs, level 2 (MINOR), type 2 (NEW_OPT)
Add option to output float-valued datasets.
Set the AFNI_FLOATIZE environment variable to YES, and the output of
3dANOVA, 3dANOVA2, and 3dANOVA3 will be stored in float format instead
of in scaled short format. [Per the request of Paul Hamilton]
18 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -test, -show_col_types, -show_cosmat, -show_fit_ts, -cormat_cutoff
also added the main help
13 Nov 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added a NIDO sphere as Displayable Object
See suma -help_nido for details.
13 Nov 2008, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT)
Added -al option to use 3dAllineate -lpa
06 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
pre-release updates:
- added many initial command-line options
- added plot_xmat_as_one toggle button
- added computation of cosine matrix and cosmat_warnings
- separated GUI code into new file gui_xmat.py
06 Nov 2008, RC Reynolds, python_module_test.py, level 2 (MINOR), type 2 (NEW_OPT)
added option -full_test
06 Nov 2008, RC Reynolds, option_list.py, level 1 (MICRO), type 2 (NEW_OPT)
added opt param to get_type_opt and get_type_list
had to modify calls in make_random_timing.py and gen_epi_review.py
03 Nov 2008, ZS Saad, 3dNLfim, level 1 (MICRO), type 2 (NEW_OPT)
Added Exp (single exponential) model
03 Nov 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Several changes
Finished -gltsym, -Rglt, and -Oglt options = add GLTs on the 3dREMLfit
command line and output those exclusively to new files.
Modified -addbase and -slibase to do censoring if input 1D files are the
same length as the uncensored matrix.
Also fixed bugs in -ABfile. Oopsie.
31 Oct 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_timing_stats option
Also, made a small change affecting timing (old results will not match).
27 Oct 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added -offset option
27 Oct 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_motion_file option
23 Oct 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Added -rout option, by popular 'demand'
23 Oct 2008, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT)
added lists_are_same function
20 Oct 2008, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
added write_text_to_file function
20 Oct 2008, RC Reynolds, afni_driver.c, level 2 (MINOR), type 2 (NEW_OPT)
added 'GETENV' to the list of DRIVE_AFNI commands
17 Oct 2008, ZS Saad, imcat, level 1 (MICRO), type 2 (NEW_OPT)
-crop is a new option for cropping an image
03 Oct 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
SUMA accepts text, images, and textures as Displayable Objects
See SUMA's interactive help for ctrl+alt+s for more information
on Displayable Objects (DOs). The new DOs are in a simple
NIML format. It is simplest to look at the script @DO.examples
for illustrations of the various forms of DOs that SUMA supports.
Sample NIML DOs (called NIDOs) are now provided with the distribution
They are called demo.*.niml.do.
03 Oct 2008, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
-viewer_position/_width/_height/_size to control window placement
See DriveSuma -help for details.
30 Sep 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
added -gltsym option
Makes it easy for the user to add GLTs without using 3dDeconvolve.
25 Sep 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
added -usetemp option
Saves REML setup matrices for various cases to tmp disk files. Is
necessary for -slibase and -Grid 5 combined, if anyone ever actually
wants to run such a case.
24 Sep 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
-addbase and -slibase options to add baseline columns to matrix
In particular, -slibase is intended for per-slice modeling of
physiological noise effects. Sucks up a lot of memory and CPU time.
23 Sep 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -remove_preproc_files option (akin to -move_preproc_files)
17 Sep 2008, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 2 (NEW_OPT)
added -labels option, for including labels in filenames
16 Sep 2008, ZS Saad, SurfDist, level 2 (MINOR), type 2 (NEW_OPT)
-node_path_do outputs the shortest path between two nodes
The shortest path(s) are stored as a SUMA Displayable Object
which can be loaded into SUMA with ctrl+alt+s or using DriveSuma.
16 Sep 2008, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
-load_do sends SUMA Displayable Objects to be rendered
See SUMA's interactive help for ctrl+alt+s for more information
on Displayable Objects.
02 Sep 2008, RW Cox, 3dAllineate, level 1 (MICRO), type 2 (NEW_OPT)
-allcostX1D option (for Chairman Z)
25 Aug 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Added residual outputs to 3dREMLfit.
22 Aug 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Add FDR curves and -?fitts options.
22 Aug 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
added DRIVE_WAIT command string
The command will be executed after the first volume is processed,
which is good for opening windows appropriate to a new dataset.
22 Aug 2008, RC Reynolds, Dimon, level 1 (MICRO), type 2 (NEW_OPT)
added -drive_wait option
21 Aug 2008, RC Reynolds, afni, level 2 (MINOR), type 2 (NEW_OPT)
added -disable_done option to safeguard real-time mode
03 Aug 2008, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -help_ana, -disp_ana, -swap_as_analyze, -swap_as_nifti, -swap_as_old
31 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 2 (NEW_OPT)
added HELLO version 2 to work as -disp_all
See 'HELLO versions' from 'serial_helper -help' for details.
See 'example E' from 'Dimon -help' for a complete testing example.
31 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
enhancements to communication with serial helper
- added 'Motion Only' to methods
- parameter methods can easily be switched per run
- SEND_VER replaces HELLO_VER as Y/N variable
31 Jul 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -num_slices option, and full real-time example E
30 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 2 (NEW_OPT)
added HELLO version 1 and -show_times option
30 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
added HELLO version 1 and show_times option
These are set via AFNI_REALTIME_SEND_VER and AFNI_REALTIME_SHOW_TIMES.
23 Jul 2008, RC Reynolds, 3dttest, level 2 (MINOR), type 2 (NEW_OPT)
added -base1_dset option, where -base1 value can vary over voxels
Added for M Beauchamp.
16 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 2 (NEW_OPT)
added -disp_all to give formatted display of 'all' mask data
This was added for P Kundu.
16 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
added choice of 'Vals to Send' to serial_helper
Can now send index,i,j,k,x,y,z,value for every value in mask.
14 Jul 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -sleep_init, -sleep_vol, -sleep_frac
These options control the timeout periods between data checks.
30 Jun 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -gen_epi_review and -no_epi_review options
By default, a drive_afni script to review EPI data is now generated.
25 Jun 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added -past_entries option
13 Jun 2008, RC Reynolds, nifticlib, level 2 (MINOR), type 2 (NEW_OPT)
added nifti_compiled_with_zlib()
13 Jun 2008, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -with_zlib, and ability to add extensions via 'file:FILENAME'
extension update added for J. Gunter
12 Jun 2008, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT)
added get_dset_reps_tr, get_default_polort, get_dset_reps_tr, max_dim_1D
also, updated find_last_space to deal with long strings
10 Jun 2008, RW Cox, 3dLocalCormat, level 2 (MINOR), type 2 (NEW_OPT)
Add -ARMA option to estimate ARMA(1,1) parameters
21 May 2008, RC Reynolds, make_stim_times.py, level 1 (MICRO), type 2 (NEW_OPT)
added -amplitudes option (for Rutvik Desai)
20 May 2008, RW Cox, plugout_drive, level 1 (MICRO), type 2 (NEW_OPT)
Make TCP/IP to 'localhost' the default. Add option '-shm' if needed.
18 May 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added options for TR-locking and storing '3dDeconvolve -nodata' examples
- added shuffle() to replace that from random (cannot produce all perms)
- added options -tr, -tr_locked and -save_3dd_cmd
- changed -stim_time option to -stim_dur
15 May 2008, ZS Saad, 3dmaskdump, level 2 (MINOR), type 2 (NEW_OPT)
added -n_rand and -n_randseed
13 May 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -set_extern_filelist option, and help for using external data files
13 May 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
gifticlib-1.0.0: initial release
includes support for (set/clear/read/write) external data files
09 May 2008, ZS Saad, 3dROIstats, level 3 (MAJOR), type 2 (NEW_OPT)
Added option -1Dformat to output results in 1D format
07 May 2008, RC Reynolds, option_list.py, level 2 (MINOR), type 2 (NEW_OPT)
added get_type_list and other accessor functions
28 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -copy_gifti_meta and -copy_DA_meta options
28 Mar 2008, RC Reynolds, gifticlib, level 1 (MICRO), type 2 (NEW_OPT)
added routines to copy MetaData
26 Mar 2008, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT)
Added -align_centers as an option to deal with very large moves
It used to be that users had to run @Align_Centers on all their
data when big moves were needed to align the surface's antaomy
to that of the experiment. This is no longer needed.
26 Mar 2008, RW Cox, 1dplot, level 2 (MINOR), type 2 (NEW_OPT)
Add -norm2 and -normx options: normalize time series before plotting
25 Mar 2008, ZS Saad, ConvertSurface, level 1 (MICRO), type 2 (NEW_OPT)
Added option -ixmat_1D to apply inverse of affine transform
24 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added GERT_Reco options (request of D Glen)
-gert_filename : specify a name for the GERT_Reco script
-gert_nz : override nz=1 in mosaic image files
-gert_to3d_prefix : specify a dataset prefix for the to3d command
21 Mar 2008, ZS Saad, 3dnvals, level 1 (MICRO), type 2 (NEW_OPT)
Added -all to 3dnvals to output all 4 dimensions.
20 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
Add -polort option, to keep Gang Chen happy.
18 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -compare_gifti option
See 'gifti_tool -help' for details, including example #7.
18 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
added comparison functions to gifticlib
17 Mar 2008, ZS Saad, lpc_align.py, level 1 (MICRO), type 2 (NEW_OPT)
Added -big_move and -partial_coverage.
-big_move is for when large displacements are needed for alignment.
-partial_coverage is for when EPI covers a portion of the brain.
14 Mar 2008, RW Cox, 3dROIstats, level 1 (MICRO), type 2 (NEW_OPT)
Sub-brick label printing (and -nobriklab option)
Per the noble Vince Hradil.
11 Mar 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 2 (NEW_OPT)
added control of hematocrit via AFNI_MODEL_D3_HCT
10 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
applied -gert_outdir in the case of dicom images
07 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Color map in surface controller can be flipped and rotated
* f key for flipping colormap
* Up/Down keys for rotating color map
* Home for home
Hit ctrl+h on Surface Controller's colormap for more help.
05 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
added '-fitts' option to produce fitted time series dataset
04 Mar 2008, RC Reynolds, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT)
added -accumulate option, to output each partial sum
for k = 0..N-1 : output[k] = sum(input[i]) over i = 0..k
03 Mar 2008, RW Cox, ++AFNI_History++ plugin, level 1 (MICRO), type 2 (NEW_OPT)
Small changes to make onscreen wordwrap match printout wordwrap
29 Feb 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added a TYPE, -type, a new level, and a string to identify each level
28 Feb 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
allow constraints on sign of deconvolved function
28 Feb 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
allow combination of penalty functions in deconvolution
28 Feb 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added -list_authors option and adjusted spacing
27 Feb 2008, RW Cox, 3dTfitter, level 3 (MAJOR), type 2 (NEW_OPT)
add deconvolution via the '-FALTUNG' option
Unlike 3dDeconvolve, this deconvolution is to find the input time
series, given the impulse response function.
25 Feb 2008, RW Cox, 1dsvd, level 2 (MINOR), type 2 (NEW_OPT)
add '-vmean' and '-vnorm' options, to mirror capabilities in 3dpc
22 Feb 2008, RW Cox, 3dpc, level 2 (MINOR), type 2 (NEW_OPT)
add '-eigonly' and '-reduce' options; output eigenvalues to a 1D file
'-eigonly' causes 3dpc to print eigenvalues to stdout and stop there.
'-reduce n pp' outputs a reduced dataset, using only the largest 'n'
eigenvalues.
20 Feb 2008, RW Cox, 1deval, level 2 (MINOR), type 2 (NEW_OPT)
add '-1D:' option, to write output that is usable on the command line
Sample usage:
1dplot `1deval -1D: -num 71 -expr 'cos(t/2)*exp(-t/19)'`
The backquotes `...` capture command's output and put this string on
the command line. The '-1D:' option formats the 1deval output so that
it is ready to be used in this way.
12 Feb 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
An option to show all of suma's environment variables
See help for -environment in suma -help.
31 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Modify plug_crender.c to obey AFNI_SLAVE_THRTIME.
24 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Add FDR curve generation to 3dANOVA.lib, 3dNLfim, 3dRegana, 3dttest.
* Fix little problems with AFNI threshold scale display as q-value alters.
* Fix bug in thd_mastery.c in assiging FDR curves to mastered sub-bricks.
* Add '-killSTAT' option to 3drefit.
23 Jan 2008, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
Older History stuff
* FDR thresh-vs-z(q) curve generation and storage in datasets.
* Display FDR q in AFNI pval label.
* Generate FDR curves automatically in 3dDeconvolve, and with
'-addFDR' option in 3drefit.
22 Jan 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added options to estimate smoothness in data for use in AlphaSim
See help options -regress_est_blur_epits and -regress_est_blur_errts.
17 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* AFNI_FLOATIZE environment variable for 3dDeconvolve.c and 3dcalc.c.
* mri_fdrize.c function for FDR-z conversion.
20 Dec 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
Older History stuff
* Clusterize reporting window.
06 Dec 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Add -jpg and -png options to 1dplot.c.
* Add thick line drawing to mri_coxplot.c (by repeated thin line drawing).
16 Nov 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Added -global_times, -local_times, and -guess_times to 3dDeconvolve.c
* For ragged 1D input files, arbitrary text starting with alphabetic
character is same as '*' for filler.
* AFNI_RESCAN_AT_SWITCH is on by default now.
* 1dplot takes a 1 row file and flips it to a column for plotting; however
,
when 2 single row files were input, they'd be catenated and THEN
flipped, producing erroneous joined plot. Now, they are flipped
THEN catenated, which does the right thing.
* Speaking of 1dplot, '-nopush' now works for multiple graphs, rather
than just for '-one'.
* Modify AlphaSim.c so that rmm defaults to -1 ==> nearest neighbors,
and so that '-seed 0' generates a custom seed.
* Add some extra text to the 'Clusterize' label (afni_setup.c) to
explain that rmm=0 means NN clustering with vmul in voxel count.
12 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Changes to bbox.c to add an arrowval index selector to the single-select
ion
mode strlist chooser (per Shruti Japee's unreasonable demand).
11 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Modify edt_filtervol.c to clip off voxels outside the fmask.
* Modify 3dmerge.c to add -1fm_noclip and -1filter_blur options.
10 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Minor changes to 3dAllineate.c: '-autoweight**1.5' sub-option;
'-autoweight' now the default for '-ls' cost function.
* Re-insert older fixes to afni.c that were lost in CVS.
20 Aug 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
Older History stuff
* First version of '-lpc' Local Pearson Correlation cost function in
3dAllineate.c, with rhombic dodecahedra as the default building bloks.
14 Aug 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Modify 3dDeconvolve.c to allow 'POLY' model to have order up to 20.
* Modify 3dLocalBistat.c to allow '-weight' option for '-pearson' statisti
c.
08 Aug 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Add threshold signage feature to AFNI threshold menu ('Pos & Neg', etc).
31 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Make -cmass the default in 3dAllineate.c.
* Also add '+clip' feature to '-autoweight' in 3dAllineate.c.
15 Feb 2007, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
High resolution image saving with ctrl+r
Very high resolution images can be created.
See suma's interactive help 'ctrl+h' for more info.
01 Dec 2005, G Chen, 3dANOVA3, level 3 (MAJOR), type 2 (NEW_OPT)
New options to run 2nd-order general linear contrasts in 3dANOVA3.
See more details on: http://afni.nimh.nih.gov/sscc/gangc/ANOVA_Mod.html
15 Jan 2003, RC Reynolds, Imon, level 3 (MAJOR), type 2 (NEW_OPT)
added connection to the realtime plugin in afni
auto-generated by afni_history on Nov 24 2009